The decapod crustaceans Macrobrachium rosenbergii and Penaeus vannamei have a very different susceptibility to White Spot Syndrome Virus infections. In order to understand and describe differences in gene expression levels following WSSV infection, we inoculated WSSV in both species and compared gene expression changes in infected and control animals from the same species, and ultimately compared changes between the two species to unravel mechanisms that may be linked with the higher tolerance to WSSV in M. rosenbergii compared to P. vannamei.